rs1363753

Positions:

• chr19-36997579-G-A
• chr19-36997579-G-C
• chr19-36997579-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000444991.6(ZNF568):​c.1888G>A​(p.Gly630Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF568 ENST00000444991.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.15

Genes affected

ZNF568 (HGNC:25392): (zinc finger protein 568) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in embryonic placenta morphogenesis and negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.060214877).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF568	NM_001204838.2	c.1888G>A	p.Gly630Ser	missense_variant	10/10		NP_001191767.1
ZNF568	NM_001204839.2	c.1696G>A	p.Gly566Ser	missense_variant	9/9		NP_001191768.1
ZNF568	XM_017026772.2	c.1888G>A	p.Gly630Ser	missense_variant	10/10		XP_016882261.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF568	ENST00000444991.6	c.1888G>A	p.Gly630Ser	missense_variant	10/10	1		ENSP00000389794
ZNF568	ENST00000591887.1	n.2057G>A		non_coding_transcript_exon_variant	2/2	1
ZNF568	ENST00000455427.7	c.1696G>A	p.Gly566Ser	missense_variant	9/9	2		ENSP00000413396

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1422384 Hom.: 0 Cov.: 39 AF XY: 0.00 AC XY: 0 AN XY: 705442

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ExAC AF: 0.00000851 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.44	T
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.21
DANN	Benign	0.87
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.013	N
LIST_S2	Benign	0.36	T;T
M_CAP	Benign	0.0027	T
MetaRNN	Benign	0.060	T;T
MetaSVM	Benign	-0.94	T
MutationTaster	Benign	1.0	P
PROVEAN	Benign	0.95	N;.
REVEL	Benign	0.046
Sift	Benign	0.47	T;.
Sift4G	Benign	0.20	T;T
Vest4		0.052
MutPred		0.23		Gain of phosphorylation at G566 (P = 0.0084);.;
MVP		0.099
ClinPred		0.052	T
GERP RS		1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1363753; hg19: chr19-37488481;